Pharmaceutical company executives, converging on Boston Thursday for the annual meeting of their largest trade association, cited growing pressures on the industry and called for faster decisions by the Food and Drug Administration on new drug applications.

The industry spent $49.5 billion on research and development last year, double the outlay in 2000, but down slightly from 2010, according to figures from the Pharmaceutical Research and Manufacturers of America, known as PhRMA.

PhRMA’s chairman, Christopher A. Viehbacher, said he brought the group’s annual meeting to Boston for the first time to showcase an innovation hub that has become a popular draw for companies in the United States and abroad. Viehbacher’s own company, France’s Sanofi SA, last year bought Cambridge biotechnology company Genzyme Corp.

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Boston is also playing host this year to the annual convention of the Biotechnology Industry Organization, called BIO, in June, and the annual conference of the American Medical Technology Association, or AdvaMed, in October. The events underscore the city’s heightened profile as a leading center for biopharmaceutical research and health care alliances.

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The growing role of those partnerships was a top theme at the PhRMA meeting as drug executives described their efforts to work with biotechnology start-ups, academic researchers, and venture capitalists to restock their drug pipelines at a time when many brand-name treatments are coming off patent and facing new competition from lower-cost generics.

“Collaboration is going to be the key success factor,’’ said Robert Hugin, chief executive of Celgene Corp., a drug company based in Summit, N.J. “There’s a recognition that everyone has the same objectives: to create great products and reduce health care costs.’’

In a report released at the PhRMA convention at the Westin Copley Place hotel Thursday, the Tufts Center for the Study of Drug Development outlined two trends that have combined to make academic-industry partnerships a more prominent feature of biomedical innovation. One is the increasing commercialization of basic research into medical products; the other is the drug industry’s search for new research and development approaches.

“Sustaining productivity in medical research is critical for the health of the economy as well as US competitiveness in the global marketplace and underscores the importance of fostering partnerships between academic medical centers and industry,’’ the report said.

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A second report from PhRMA, focused more narrowly on Massachusetts, said the state has hosted 3,984 clinical trials since 1999. That includes 2,073 targeting the top six chronic diseases: asthma, cancer, diabetes, heart disease, mental illness, and stroke.

Industry leaders said they were prepared to contribute higher fees to fund the FDA’s review of new drug candidates under the proposed reauthorization of the Prescription Drug User Fee Act, which is making its way through Congress. The goal would be a create a faster and more efficient review process without compromising safety, they said.

“We are willing to pay more in user fees so the FDA can hire more people,’’ Viehbacher told more than 300 executives at the meeting. In return, he said, industry leaders would like to see “some level of predictability in regulatory outcomes.’’

John Lechleiter, chief executive of drug maker Eli Lilly & Co., based in Indianapolis, said the number of FDA drug approvals rose to 30 in 2011 from 22 in 2010 but had totaled just 89 from 2006 to 2010. Industry executives want that number to grow.

In addition to generics, the pharmaceutical industry is being squeezed by government spending cuts, as well as institutional investors who are clamoring for drug makers to divert research dollars to buy back shares, speakers at the PhRMA meeting said.

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Lamenting that the economic crisis created huge deficits in Western countries, especially in Europe, Viehbacher said, “We’re clearly seeing the impact of austerity measures on our industry’’ as governments rein in support for development and reimbursements of new medicines.

At the same time, he said, the industry expects to lose $60 billion to $80 billion in annual sales to generic rivals in the next few years as expensive branded therapies lose their patent protection. While that will save money for patients and health care systems, he said, it will intensify pressure on drug makers.

“Welcome to the patent cliff,’’ he said.

Governor Deval Patrick, welcoming the trade group to Boston, said Massachusetts stands ready to help companies boost the impact of their research dollars by tapping into the state’s network of cutting-edge biotechnology companies, academic medical centers, and venture capital firms. A growing number of global pharmaceutical giants, including Sanofi and Switzerland’s Novartis AG, have increased their presence here during the past few years.

Noting that his administration has established a 10-year, $1 billion initiative to attract life sciences companies and help them grow, Patrick said, “I know the current fashion is to emphasize one’s austerity measures. But I emphasize our investments.’’

State funding has drawn further investments from the industry, Patrick said.

“For every $1 of public money invested, we have attracted more than $3 of private investment and created thousands of jobs,’’ he said.